Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_074201292.1 BUQ81_RS05080 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_900141795.1:WP_074201292.1 Length = 365 Score = 336 bits (862), Expect = 5e-97 Identities = 173/359 (48%), Positives = 236/359 (65%), Gaps = 6/359 (1%) Query: 10 VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69 V + PY GKPI E+ RE GL + KLASNENPLG A+ +A+ E+ RYPD Sbjct: 10 VEQLIPYQPGKPIEELQRELGLTRVS--KLASNENPLGASPQVISALEKASQEIARYPDG 67 Query: 70 NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129 +A+ LK L+ + V + + +GNGSN++LE+ AF G ++Y Q++FAVY L+T+ Sbjct: 68 SAYALKRRLAAFHSVEPEMIVVGNGSNEVLELVVRAFAGPGDEVIYDQHAFAVYPLSTRA 127 Query: 130 LGARAIVVPAVK-YGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRH 188 GA +VVP+ + + HDLDAM AAV++ TRLIF+ANPNNPTGT+ + E F+ VP Sbjct: 128 AGATGVVVPSSEGFAHDLDAMAAAVTNRTRLIFLANPNNPTGTYFGRSEFERFMQAVPER 187 Query: 189 VVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDL 248 V+VVLDEAY E++ + D + RY NL+V+RTFSK +GLA LR+G+ +A+PE+ D Sbjct: 188 VLVVLDEAYFEFVSHSDKLDGSQLLDRYANLVVTRTFSKVYGLASLRIGYLLARPEIADY 247 Query: 249 LNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNF 308 LNRVR+PFN + AQ AA+AAL+D+AF+++S A N + L D+ LE +P+ GNF Sbjct: 248 LNRVREPFNTSHFAQLAAMAALDDQAFVQRSVAYNREALAELKATADRFALETLPAYGNF 307 Query: 309 VLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTL 367 + V G + N VN LLKQGVIVRP+ YG+ QWLRI+ G PEE ALE L Sbjct: 308 LTVHFGPE---ANAVNNALLKQGVIVRPLAGYGMAQWLRISTGTPEEQAHLAEALETIL 363 Lambda K H 0.318 0.135 0.385 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 402 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 370 Length of database: 365 Length adjustment: 30 Effective length of query: 340 Effective length of database: 335 Effective search space: 113900 Effective search space used: 113900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory